scRNA-seq analysis of aged immune system in mice

Aging is associated with systemic chronic inflammation (inflammaging) that leads to impaired physiological functions and vulnerability to several diseases. However, underlying alterations in aged immune system resulting in gradual loss of immune fitness4 remain unclear. Using a combination of single-cell RNA/TCR/BCR-sequencing and extensive FACS/CyTOF-based validation, we comprehensively characterize age-associated alterations in immune cells in 4 mouse organs and human blood. We identified both organ-specific and common changes in immune cell populations and their transcriptional programs and found age-associated subpopulation of CD8+ T cells marked with expression of GZMK. Overall design: Droplet-based 5' end massively parallel single-cell RNA sequencing was performed by isolating mouse CD45+ cells sorted by FACS from the spleen, peritoneal cavity, the lungs and the liver and libraries (5'GEX, TCR, and BCR enrichment libraries) were prepared using Chromium Single Cell 5' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using NovaSeq S4 sequencers. 3 biologically independent mice per age were pooled, processed and sequenced.